Methods in Ecology and Evolution

Papers
(The TQCC of Methods in Ecology and Evolution is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-02-01 to 2024-02-01.)
ArticleCitations
Robustness of linear mixed‐effects models to violations of distributional assumptions483
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML350
Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package309
metan: An R package for multi‐environment trial analysis264
geomorph v4.0 and gmShiny: Enhanced analytics and a new graphical interface for a comprehensive morphometric experience202
ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions178
ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches165
Predicting into unknown space? Estimating the area of applicability of spatial prediction models131
An empirical evaluation of camera trap study design: How many, how long and when?107
Improving Landsat predictions of rangeland fractional cover with multitask learning and uncertainty96
A field and video annotation guide for baited remote underwater stereo‐video surveys of demersal fish assemblages92
Redundancy analysis: A Swiss Army Knife for landscape genomics91
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish91
Methods for testing publication bias in ecological and evolutionary meta‐analyses90
Deep learning‐based methods for individual recognition in small birds89
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists83
Towards a more balanced combination of multiple traits when computing functional differences between species80
A deep active learning system for species identification and counting in camera trap images77
phyr: An r package for phylogenetic species‐distribution modelling in ecological communities69
Network measures in animal social network analysis: Their strengths, limits, interpretations and uses69
rTPC and nls.multstart: A new pipeline to fit thermal performance curves in r67
Operationalizing ecological connectivity in spatial conservation planning with Marxan Connect67
phyloregion: R package for biogeographical regionalization and macroecology65
Functional diversity metrics using kernel density n‐dimensional hypervolumes64
adiv: An r package to analyse biodiversity in ecology59
SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology58
The Movebank system for studying global animal movement and demography55
Automatic image‐based identification and biomass estimation of invertebrates53
The use of Bayesian priors in Ecology: The good, the bad and the not great53
Generalized hidden Markov models for phylogenetic comparative datasets52
The welfare and ethics of research involving wild animals: A primer51
embarcadero: Species distribution modelling with Bayesian additive regression trees in r51
On the measurement of microclimate49
Unbiased population heterozygosity estimates from genome‐wide sequence data49
GCM compareR: A web application to assess differences and assist in the selection of general circulation models for climate change research48
Systematic review of modelling assumptions and empirical evidence: Does parasite transmission increase nonlinearly with host density?46
Deep learning as a tool for ecology and evolution46
Plant and root‐zone water isotopes are difficult to measure, explain, and predict: Some practical recommendations for determining plant water sources45
Automated detection of wildlife using drones: Synthesis, opportunities and constraints44
DeepForest: A Python package for RGB deep learning tree crown delineation44
Quality control for modern bone collagen stable carbon and nitrogen isotope measurements43
A quick, easy and non‐invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons39
The Flora Incognita app – Interactive plant species identification39
Spatial thinning and class balancing: Key choices lead to variation in the performance of species distribution models with citizen science data39
A practical guide to question formation, systematic searching and study screening for literature reviews in ecology and evolution38
Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models38
Meta‐analysis of primary producer amino acid δ15N values and their influence on trophic position estimation38
Inferring individual fate from aquatic acoustic telemetry data37
Outstanding challenges and future directions for biodiversity monitoring using citizen science data37
An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data37
Autocorrelation‐informed home range estimation: A review and practical guide36
ubms: An R package for fitting hierarchical occupancy and N‐mixture abundance models in a Bayesian framework35
The potential and practice of arboreal camera trapping33
Robust ecological analysis of camera trap data labelled by a machine learning model33
Machine learning and deep learning—A review for ecologists32
dsmextra: Extrapolation assessment tools for density surface models32
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture32
Integrating airborne remote sensing and field campaigns for ecology and Earth system science32
A standardisation framework for bio‐logging data to advance ecological research and conservation32
ALPACA: A fast and accurate computer vision approach for automated landmarking of three‐dimensional biological structures32
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes32
Permutation tests for hypothesis testing with animal social network data: Problems and potential solutions31
Replication in field ecology: Identifying challenges and proposing solutions31
Phylogenetically aligned component analysis30
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions30
assignR: An r package for isotope‐based geographic assignment30
Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization30
track2KBA: An R package for identifying important sites for biodiversity from tracking data30
Navigating the temporal continuum of effective population size30
HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices30
A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry29
Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices29
Survey coverage, recording duration and community composition affect observed species richness in passive acoustic surveys29
The accuracy of phenology estimators for use with sparsely sampled presence‐only observations28
The Australian Acoustic Observatory28
Unifying individual differences in personality, predictability and plasticity: A practical guide28
Spot size, distance and emissivity errors in field applications of infrared thermography28
spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models28
Acoustic indices perform better when applied at ecologically meaningful time and frequency scales27
rasterdiv—An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back27
The Purr‐fect Catch: Using accelerometers and audio recorders to document kill rates and hunting behaviour of a small prey specialist27
Detecting plant species in the field with deep learning and drone technology27
Parametrizing diffusion‐taxis equations from animal movement trajectories using step selection analysis26
metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality26
Defining and evaluating predictions of joint species distribution models26
Unsupervised acoustic classification of individual gibbon females and the implications for passive acoustic monitoring26
Overcoming the pitfalls of merging dietary metabarcoding into ecological networks26
PICT: A low‐cost, modular, open‐source camera trap system to study plant–insect interactions25
The neglected impact of tracking devices on terrestrial arthropods25
Scaling methods in ecological modelling25
The effects of lipid extraction on δ13C and δ15N values and use of lipid‐correction models across tissues, taxa and trophic groups25
Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: Lessons from natural assemblages25
Improving the accuracy of land cover classification in cloud persistent areas using optical and radar satellite image time series24
Phylogenetic multilevel meta‐analysis: A simulation study on the importance of modelling the phylogeny24
Analysing economic costs of invasive alien species with the invacost r package24
Determination of optimal flight altitude to minimise acoustic drone disturbance to wildlife using species audiograms24
ML‐morph: A fast, accurate and general approach for automated detection and landmarking of biological structures in images24
Open‐source, low‐cost modular GPS collars for monitoring and tracking wildlife23
Existing and emerging uses of drones in restoration ecology23
Detection dogs in nature conservation: A database on their world‐wide deployment with a review on breeds used and their performance compared to other methods23
Hidden Markov models: Pitfalls and opportunities in ecology23
Calculating effect sizes in animal social network analysis23
Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife23
actel: Standardised analysis of acoustic telemetry data from animals moving through receiver arrays23
ForestScanner: A mobile application for measuring and mapping trees with LiDAR‐equipped iPhone and iPad23
Efficient, automated and robust pollen analysis using deep learning22
r3PG – An r package for simulating forest growth using the 3‐PG process‐based model22
viewshed3d: An r package for quantifying 3D visibility using terrestrial lidar data22
Double‐tagging scores of seabirds reveals that light‐level geolocator accuracy is limited by species idiosyncrasies and equatorial solar profiles22
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation22
Multi‐species occupancy models as robust estimators of community richness22
Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance22
A workflow for accurate metabarcoding using nanopore MinION sequencing22
The way bioclimatic variables are calculated has impact on potential distribution models22
Listening and watching: Do camera traps or acoustic sensors more efficiently detect wild chimpanzees in an open habitat?22
A new joint species distribution model for faster and more accurate inference of species associations from big community data21
Refined Shortest Paths (RSP): Incorporation of topography in space use estimation from node‐based telemetry data21
graph4lg: A package for constructing and analysing graphs for landscape genetics in R21
Estimating encounter location distributions from animal tracking data21
phenofit: An R package for extracting vegetation phenology from time series remote sensing21
Analysis of temporal patterns in animal movement networks21
Wavelet filters for automated recognition of birdsong in long‐time field recordings21
A methodological guide for translating study instruments in cross‐cultural research: Adapting the ‘connectedness to nature’ scale into Chinese20
Incorporating climate velocity into the design of climate‐smart networks of marine protected areas20
Reliably predicting pollinator abundance: Challenges of calibrating process‐based ecological models20
Interactions in statistical models: Three things to know20
A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems20
Identifying flow modules in ecological networks using Infomap20
Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms20
Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation20
Congruence of local ecological knowledge (LEK)‐based methods and line‐transect surveys in estimating wildlife abundance in tropical forests19
Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction19
AIDE: Accelerating image‐based ecological surveys with interactive machine learning19
A cost‐effective video system for a rapid appraisal of deep‐sea benthic habitats: The Azor drift‐cam19
A spatial capture–recapture model to estimate call rate and population density from passive acoustic surveys19
nosoi: A stochastic agent‐based transmission chain simulation framework in r19
Leaving the area under the receiving operating characteristic curve behind: An evaluation method for species distribution modelling applications based on presence‐only data19
Null models for animal social network analysis and data collected via focal sampling: Pre‐network or node network permutation?18
Telemetry‐validated nitrogen stable isotope clocks identify ocean‐to‐estuarine habitat shifts in mobile organisms18
The In situ Plankton Assemblage eXplorer (IPAX): An inexpensive underwater imaging system for zooplankton study18
The power of forecasts to advance ecological theory18
Marine artificial light at night: An empirical and technical guide18
scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python18
Schrödinger's phenotypes: Herbarium specimens show two‐dimensional images are both good and (not so) bad sources of morphological data18
Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches18
Nemo‐age: Spatially explicit simulations of eco‐evolutionary dynamics in stage‐structured populations under changing environments17
Animal social networks: Towards an integrative framework embedding social interactions, space and time17
A unifying framework for quantifying and comparing n‐dimensional hypervolumes17
Determining marine bioregions: A comparison of quantitative approaches17
Visual TreeCmp: Comprehensive Comparison of Phylogenetic Trees on the Web17
Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package17
On the relationship of fractal geometry and tree–stand metrics on point clouds derived from terrestrial laser scanning17
Multi‐output Gaussian processes for species distribution modelling16
Why did the animal turn? Time‐varying step selection analysis for inference between observed turning‐points in high frequency data16
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies16
Protein quantification in ecological studies: A literature review and empirical comparisons of standard methodologies16
Bulk arthropod abundance, biomass and diversity estimation using deep learning for computer vision16
From alpha to beta functional and phylogenetic redundancy16
Internet on animals: Wi‐Fi‐enabled devices provide a solution for big data transmission in biologging16
flexsdm: An r package for supporting a comprehensive and flexible species distribution modelling workflow16
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists16
Optimizing aerial imagery collection and processing parameters for drone‐based individual tree mapping in structurally complex conifer forests15
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature15
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity15
A machine learning approach for classifying and quantifying acoustic diversity15
moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in r15
The r toolbox grainscape for modelling and visualizing landscape connectivity using spatially explicit networks15
Optimising sample sizes for animal distribution analysis using tracking data15
The omnistat: A flexible continuous‐culture system for prolonged experimental evolution15
Tracking the temporal dynamics of insect defoliation by high‐resolution radar satellite data15
steps: Software for spatially and temporally explicit population simulations15
The consequences of checking for zero‐inflation and overdispersion in the analysis of count data15
Study becomes insight: Ecological learning from machine learning15
A novel and efficient method for wood–leaf separation from terrestrial laser scanning point clouds at the forest plot level14
Opportunities and risks in the use of drones for studying animal behaviour14
Disentangling effects of climate and land use on biodiversity and ecosystem services—A multi‐scale experimental design14
Machine learning applications in river research: Trends, opportunities and challenges14
Methodology matters for comparing coarse wood and bark decay rates across tree species14
Revisiting animal photo‐identification using deep metric learning and network analysis14
Exploiting the full potential of Bayesian networks in predictive ecology14
bdc: A toolkit for standardizing, integrating and cleaning biodiversity data14
hyperoverlap: Detecting biological overlap in n‐dimensional space14
Neural ordinary differential equations for ecological and evolutionary time‐series analysis14
MEDI: Macronutrient Extraction and Determination from invertebrates, a rapid, cheap and streamlined protocol14
HumBug – An Acoustic Mosquito Monitoring Tool for use on budget smartphones14
Quantifying effects of tracking data bias on species distribution models14
Automated retrieval of information on threatened species from online sources using machine learning14
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets14
Quantifying carbon in tree bark: The importance of bark morphology and tree size14
Infectious disease phylodynamics with occurrence data13
An evaluation of platforms for processing camera‐trap data using artificial intelligence13
A primer on partially observable Markov decision processes (POMDPs)13
Advancing diet reconstruction in fish eye lenses13
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation13
ROBITT: A tool for assessing the risk‐of‐bias in studies of temporal trends in ecology13
A novel red‐edge spectral index for retrieving the leaf chlorophyll content13
A practical approach to measuring the biodiversity impacts of land conversion13
Innovations in movement and behavioural ecology from camera traps: Day range as model parameter13
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists13
One leaf for all: Chemical traits of single leaves measured at the leaf surface using near‐infrared reflectance spectroscopy12
Incorporating time into the traditional correlational distributional modelling framework: A proof‐of‐concept using the Wood Thrush Hylocichla mustelina12
Sashimi: A toolkit for facilitating high‐throughput organismal image segmentation using deep learning12
Calibration chain transformation improves the comparability of organic hydrogen and oxygen stable isotope data12
poems: R package for simulating species' range dynamics using pattern‐oriented validation12
State‐space models for ecological time‐series data: Practical model‐fitting12
cxr: A toolbox for modelling species coexistence in R12
Comparing traditional and Bayesian approaches to ecological meta‐analysis12
Validating ATLAS: A regional‐scale high‐throughput tracking system12
SAFE Acoustics: An open‐source, real‐time eco‐acoustic monitoring network in the tropical rainforests of Borneo12
A standardised biologging approach to infer parturition: An application in large herbivores across the hider‐follower continuum12
Count transformation models12
Constructing and analysing time‐aggregated networks: The role of bootstrapping, permutation and simulation12
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution12
Rcompadre and Rage—Two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life‐history traits from matrix population models12
Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance12
Integrated population models poorly estimate the demographic contribution of immigration12
Dynamic visualisation of million‐tip trees: The OneZoom project11
Shannon entropy as a robust estimator of Zipf's Law in animal vocal communication repertoires11
Mooring scientific instruments on the seabed—Design, deployment protocol and performance of a recoverable frame for acoustic receivers11
bRacatus: A method to estimate the accuracy and biogeographical status of georeferenced biological data11
Revisiting the minimum set cover, the maximal coverage problems and a maximum benefit area selection problem to make climate‐change‐concerned conservation plans effective11
Assessing the performance and efficiency of environmental DNA/RNA capture methodologies under controlled experimental conditions11
Analytical models for β‐diversity and the power‐law scaling of β‐deviation11
Chipper: Open‐source software for semi‐automated segmentation and analysis of birdsong and other natural sounds11
Standardized nuclear markers improve and homogenize species delimitation in Metazoa11
msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r11
A multi‐platform package for the analysis of intra‐ and interspecific trait evolution11
RUbble Biodiversity Samplers: 3D‐printed coral models to standardize biodiversity censuses11
Solving the sample size problem for resource selection functions11
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management11
Modelling the joint effects of body size and microclimate on heat budgets and foraging opportunities of ectotherms11
Complementary sampling methods for coral histology, metabolomics and microbiome11
allodb: An R package for biomass estimation at globally distributed extratropical forest plots11
A Raspberry Pi‐based camera system and image processing procedure for low cost and long‐term monitoring of forest canopy dynamics11
A practical method for evaluating spatial biodiversity offset scenarios based on spatial conservation prioritization outputs11
Conditional repeatability and the variance explained by reaction norm variation in random slope models11
Merging computational fluid dynamics and machine learning to reveal animal migration strategies10
Extending Bayesian Elo‐rating to quantify the steepness of dominance hierarchies10
Positional errors in species distribution modelling are not overcome by the coarser grains of analysis10
CMRnet: An r package to derive networks of social interactions and movement from mark–recapture data10
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data10
Mapping forest leaf area density from multiview terrestrial lidar10
Fast model‐based ordination with copulas10
maxnodf: An R package for fair and fast comparisons of nestedness between networks10
Modelling and inference for the movement of interacting animals10
Tree‐based inference of species interaction networks from abundance data10
mcera5: Driving microclimate models with ERA5 global gridded climate data10
Terrestrial laser scanning to reconstruct branch architecture from harvested branches10
Estimating species relative abundances from museum records10
A customizable, low‐cost optomotor apparatus: A powerful tool for behaviourally measuring visual capability10
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